ABSTRACT: Head and neck squamous cell carcinoma (HNSCC) is the 7th most prevalent cancer globally, resulting in 930,000 new cases and 467,000 deaths annually. Alongside tobacco and alcohol use, human papillomavirus (HPV) infection contributes to HNSCC development. Regardless of their clinical stage or location, these tumors exhibit significant heterogeneity in gene expression and treatment response. While immunotherapy has revolutionized treatment approaches for many cancers, its impact on HNSCC remains limited. This suggests aspects of HNSCC tumor immunology – including the role HPV plays in immune dysregulation – are not well understood. Thus, the objective of this research is to develop, validate, and implement advanced computational tumor phenotyping techniques to characterize HNSCC at multiple levels of biological organization. Our approach involves high-throughput analysis of quantitative features from both radiology images (i.e., radiomics) and digital pathology images (i.e., pathomics) to generate a multiscale depiction of the HNSCC phenotype. We hypothesize that tumor-specific radiopathomic expression patterns of HNSCC are connected to fundamental biological and immunomolecular processes driving therapeutic resistance. In Aim 1, the prognostic value of radiomics will be evaluated in both HPV+ and HPV− HNSCC patients treated with radiotherapy as part of a previously conducted prospective clinical trial (NCT01908504). Changes in radiomic expression after initial 20 Gy will be quantified via data assimilation of PET/CT imaging and stochastic models of tumor dynamics. In Aim 2, the tumor immune microenvironment of these patients will be characterized via pathomic analysis. Single-cell interactions will be measured between different immune compositions and compared to single-cell transcriptomics data to gain mechanistic insight into the genes driving pathomic expression. Radiomics (Aim 1) and pathomics (Aim 2) will each be experimentally confirmed and mechanistically validated in novel carcinogen-induced and genetically engineered mouse models that co-evolve with an intact immune system, where we will dissect mechanisms of treatment resistance and interrogate immune dysregulation in mice that spontaneously develop HPV+ vs. HPV− HNSCC. In Aim 3, our scientific findings will be independently tested in an ongoing prospective interventional study (NCT04667585) to evaluate radiopathomic expression as a potential biomarker to guide adaptive therapy for HPV+ HNSCC. Candidate biomarkers identified in NCT01908504 will be independently tested in NCT04667585 to provide an unbiased evaluation of their prognostic value. The rationale for these studies is to enhance understanding of HNSCC biology to guide improved treatment approaches for this urgent, unmet clinical need. By leveraging innovative radiopathomic strategies, novel clinical trial data, and complementary mechanistic interrogation, our proposed research will be an important advancement in comput...